crossing96/oncoscreening huggingface dataset:
Efficient bladder cancer diagnosis using an improved RIME algorithm with Orthogonal Learning.	Bladder cancer (BC) diagnosis presents a critical challenge in biomedical research, necessitating accurate tumor classification from diverse datasets for effective treatment planning. This paper introduces a novel wrapper feature selection (FS) method that leverages a hybrid optimization algorithm combining Orthogonal Learning (OL) with a rime optimization algorithm (RIME), termed mRIME. The mRIME algorithm is designed to avoid local optima, streamline the search process, and select the most relevant features without compromising classifier performance. It also introduces mRIME-SVM, a novel hybrid model integrating modified mRIME for FS with Support Vector Machine (SVM) for classification. The mRIME algorithm is employed as an FS method and is also utilized to fine-tune the hyperparameters of it the It SVM, enhancing the overall classification accuracy. Specifically, mRIME navigates complex search spaces to optimize FS without compromising classifier performance. Evaluated on eight diverse BC datasets, mRIME-SVM outperforms popular metaheuristic algorithms, ensuring precise and reliable diagnostic outcomes. Moreover, the proposed mRIME was employed for tackling global optimization problems. It has been thoroughly assessed using the IEEE Congress on Evolutionary Computation 2022 (CEC'2022) test suite. Comparative analyzes with Gray wolf optimization (GWO), Whale optimization algorithm (WOA), Harris hawks optimization (HHO), Golden Jackal Optimization (GJO), Hunger Game optimization algorithm (HGS), Sinh Cosh Optimizer (SCHO), and the original RIME highlight mRIME's competitiveness and efficacy across diverse optimization tasks. Leveraging mRIME's success, mRIME-SVM achieves high classification accuracy on nine BC datasets, surpassing existing models. Results underscore mRIME's competitiveness and applicability across diverse optimization tasks, extending its utility to enhance BC classification. This study contributes to advancing BC diagnostics with a robust computational framework, promising broader applications in bioinformatics and AI-driven medical research.	bladder
Bladder cancer incidence and mortality among men with and without castration therapy for prostate cancer - a nation-wide cohort study.	BACKGROUND AND PURPOSE: Bladder cancer (BC) is a common malignancy in the Western World with men being diagnosed almost four times as often as women. The etiology of bladder cancer may involve sex hormones. Prostate cancer (PCa) patients treated with chemical castration, such as androgen deprivation therapy, or surgical castration, may therefore have a lower risk of developing bladder cancer. PATIENTS/MATERIAL AND METHODS: In a nation-wide population-based cohort study using national Danish registry data, we included a cohort of men with a first-time PCa diagnosis between 2002 and 2018 divided according to antihormonal treatment in the first year after PCa diagnosis and a comparison cohort consisting of 10 age-matched persons for each PCa patient. Each individual was followed from 1 year after PCa diagnosis until death or end of follow-up. We computed cumulative incidences (risk) and hazard ratios (HRs) for BC. In a second cohort analysis, we determined overall survival and BC-specific mortality, determined from date of BC diagnosis until death. RESULTS AND INTERPRETATION: We included 48,776 PCa patients of whom 13,592 were treated with chemical castration, 2,261 with surgical castration, and 32,923 received no antihormonal treatment. The 5-year risk of BC for each PCa group was 1.1%, 0.7%, and 1.3%, respectively, corresponding to an adjusted HR of 1.13 (95% CI 0.98; 1.31), 0.95 (95% CI 0.62; 1.47), and 1.18 (95% CI 1.09; 1.28) compared to individuals without PCa. Patients receiving antihormonal treatment had a slightly lower incidence of BC compared to individuals without PCa, however, this was not supported by the HRs. The treatment, however, was not associated with overall survival.	bladder
Lymphatic embolization for early post-operative lymphatic leakage after radical cystectomy for bladder cancer.	BACKGROUND AND OBJECTIVE: Although radical cystectomy (RC) with pelvic lymph node dissection (PLND) is the standard treatment of muscle invasive bladder cancer, it may cause lymphatic leakage. Recent studies describe lymphatic embolization (LE) as an option to manage post-operative lymphatic leakage. Hence, this study evaluated the outcome of LE in patients receiving RC and analyzed factors associated with outcomes. METHODS: This was a retrospective analysis of patients who underwent LE after RC for bladder cancer between August 2017 and June 2023. The data was assessed for analysis at January 2024. The patients were divided into a clinical success group and a clinical failure group. Clinical failure was defined as the following: 1) those who required drainage catheter placement >7 days after LE, 2) those who needed re-intervention before catheter removal, and 3) those who experienced adverse events associated with LE. Logistic regression analysis was performed to identify the factors associated with outcomes of LE. KEY FINDINGS AND LIMITATIONS: We analyzed 45 patients who underwent LE after RC. Twenty-eight (62.2%) patients were identified as clinically successful. Four patients required re-embolization, but none required more than two sessions of intervention. Three patients experienced lymphatic complications after LE. In multivariable analysis, maximal daily drainage volume of >1,000 mL/day (odds ratio [OR] = 4.729, 95% confidence interval [CI]: 1.018-21.974, p = 0.047) and diabetes mellitus (DM) (OR = 4.571, 95% CI: 1.128-18.510, p = 0.033) were factors associated with LE outcome. CONCLUSIONS AND CLINICAL IMPLICATIONS: Our results suggest LE as a potentially effective procedure for controlling post-operative lymphatic leaks after RC, with few minor side effects. Patients exceeding a daily drainage of 1,000mL/day or with a medical history of DM have a higher risk for re-intervention and clinical failure after LE.	bladder
The mental and emotional status after radical cystectomy and different urinary diversion orthotopic bladder substitution versus external urinary diversion after radical cystectomy: A propensity score-matched study.	OBJECTIVES: The quality of life in patients undergoing radical cystectomy and urinary diversion is gaining importance. Nowadays a broad consensus about the best urinary diversion does not exist. This study presents an all-round analysis of the impact of two types of urinary diversion on life's psycho-social aspects in patients undergoing radical cystectomy. METHODS: This is an observational, single-centre, prospective study. Eligible participants underwent radical cystectomy and urinary diversion for bladder cancer in our department from January 2020 and February 2024. Of 130 included patients, 90 (45 with Bricker's ureteroileocutaneostomy and 45 received orthotopic bladder replacement) patients were matched and the study groups were well balanced for the baseline-matched variables. Patients completed 4 questionnaires (EORTC QLQ-C30, PGWBI, HADS, PSQI) at three different times: before the surgical procedure, and at 3 and 12 months. RESULTS: Time shows a statistically significant effect (p < 0.0005) on four of the five functional scales explored (Physical Functioning, Role Functioning, Emotional Functioning, Social Functioning), and for all the nine symptoms/items' scales (p < 0.0005) and the Global Health Status (p = 0.003) in EORTC QLQ-C30. Neobladder's group shows a statistically significant improvement on the scales of Physical Functioning, Role Functioning, and Social Functioning, and for symptoms of nausea (p = 0.0027), pain (p = 0.0005), dyspnea (p = 0.012), insomnia (p = 0.004), constipation (p = 0.003). CONCLUSION: We do not find a better urinary diversion in absolute terms. Neobladder obtained better results only for specific items and features. The urinary diversion's choice must be made in concert by the patient, the caregiver, and health professionals with adequate counseling.	bladder
Evaluation of a Cytology-Molecular Co-Test in Liquid-Based Cytology-Processed Urine for Defining Indeterminate Categories of the Paris System.	"INTRODUCTION: Urine cytology using the Paris system (TPS) classification is useful for the detection and monitoring of bladder urothelial carcinoma (UC). However, the categories ""atypical urothelial cells"" (AUCs) and ""suspicious for high-grade urothelial carcinoma"" (SHGUC) do not establish a clear diagnosis. This pilot study aimed to investigate whether the presence of mutations in fibroblast growth factor receptor 3 (FGFR3) and telomerase reverse transcriptase (TERT) genes, in urine processed with liquid-based cytology (LBC) could enhance the diagnostic performance of cytology, particularly in defining the indeterminate categories of AUC and SHGUC. METHODS: Urine samples from 82 UC patients with primary tumors or under surveillance and 10 healthy individuals were examined. The ThinPrep method was used for cytology followed by DNA isolation from urine sediments. Targeted molecular analysis was achieved in 70 cases (63 patients and 7 controls) for exons 7 and 10 of the FGFR3 gene and the TERT gene promoter (pTERT), using PCR and Sanger sequencing. Molecular results were correlated with TPS cytology categories and validated by histopathological findings following cystoscopy. RESULTS: In healthy subjects, cytology was negative for high-grade urothelial carcinoma (NHGUC) and no mutations were found. No mutations were found in patients with NHGUC cytology, except for one case with equivocal cystoscopy that carried a pTERT mutation. In high-grade urothelial carcinoma cytology (HGUC) (15/20, 75%) of the cases with histologically confirmed UC, molecular analysis revealed the presence of pTERT without FGFR3 mutations. In SHGUC and AUC cytology, FGFR3 and/or pTERT mutations were detected in 3/4 (75%) and 4/4 (100%) histologically confirmed UC cases, respectively. Cytology sensitivity was 85.7% increasing to 100% with the combined cytology-molecular test, whereas specificity remained unchanged at 86.3%. CONCLUSIONS: This pilot study suggests that the incorporation of FGFR3/pTERT molecular testing in urine LBC could enhance the diagnostic value of cytology by diagnosing bladder urothelial carcinoma in indeterminate cytology categories."	bladder
Image-Guided Brachytherapy for Pediatric Bladder and/or Prostate Rhabdomyosarcoma: Toward an Increased Personalization of Treatment.	PURPOSE: Rhabdomyosarcoma (RMS) is the most common soft tissue cancer in children. Around 15% of RMS involve the bladder and/or prostate (BP). Overall survival is around 85%. After chemotherapy, patients receive local treatment based on surgery and/or radiation therapy. In recent decades, image guidance and pulsed-dose rate (PDR) brachytherapy have made it possible to personalize treatment and reduce radiation-related toxicity while maintaining good tumor control. We report one of the largest series of image guided brachytherapy for pediatric RMS BP. METHODS AND MATERIALS: The clinical and dosimetric parameters of children treated with brachytherapy for BP RMS between July 2014 and September 2020 were retrospectively reviewed. Patients were treated with a multimodal conservative approach, combining partial conservative surgery (preservation of the bladder neck and urethra), followed by an interstitial brachytherapy procedure. Iridium-192 PDR treatment was administered on the basis of computed tomography and magnetic resonance imaging planning. Toxicities were reported according to version 4.0 of the Common Terminology Criteria for Adverse Events. RESULTS: A total of 75 patients were identified, with a median age of 29 months (range, 2-84) at diagnosis. The median brachytherapy dose was 60.06 Gy (143 pulses, 0.42 Gy/pulse). With a median follow-up of 44.1 months (range, 0.7-90), the 5-year overall survival and progression-free survival rates were 97.3% and 92%, respectively. Median D(50%) for the bladder and D(1cc) for the rectum were 38.6 Gy and 49 Gy, respectively. The 5-year probability of survival without severe late urinary toxicity (grade 3 or higher) was estimated at 78.8% (95% CI, 68.1-91.1). A total of 9.3% of children experienced grade 2 or 3 late rectal toxicity. CONCLUSIONS: Image guided PDR brachytherapy offers personalized treatment for pediatric BP RMS, with a favorable therapeutic index. No prognostic factors for urinary toxicity have been identified. Multicenter studies with larger numbers of patients are needed to clarify these data.	bladder
Are androgen receptor agonists a treatment option in bladder cancer?	Sex-related differences in bladder cancer incidence and progression infer a role for sex hormones and their cognate receptors in this disease. In part due to the oncogenic role of androgen receptor signaling in prostate cancer, the focus of most preclinical and clinical research to-date has been on the potential pro-tumorigenic action of androgens in urothelial cancers. However, clinical studies of androgen receptor antagonism have yielded minimal success. In this review, we explore the tumor suppressor role of androgen receptor in bladder cancer and discuss how it might be harnessed therapeutically.	bladder
Follow-up strategies after trimodal treatment for muscle-invasive bladder cancer: a systematic review.	PURPOSE: Optimal follow-up strategies following trimodal treatment for muscle invasive bladder cancer play a crucial role in detecting and managing relapse and side-effects. This article provides a comprehensive summary of the patterns and risk factors of relapse, functional outcomes, and follow-up protocols. METHODS: A systematic literature search on PubMed and review of current guidelines and institutional follow-up protocols after trimodal therapy were conducted. RESULTS: Out of 200 identified publications, 43 studies (28 retrospective, 15 prospective) were selected, encompassing 7447 patients (study sizes from 24 to 728 patients). Recurrence rates in the urinary bladder varied between 14-52%; 3-16% were muscle-invasive while 11-36% were non-muscle invasive. Nodal recurrence occurred at 13-16% and distant metastases at 15-35%. After 5 and 10 years of follow-up, around 60-85% and 45-75% of patients could preserve their bladder, respectively. Various prognostic risk factors associated with relapse and inferior survival were proposed, including higher disease stage (> c/pT2), presence of extensive/multifocal carcinoma in situ (CIS), hydronephrosis, multifocality, histological subtypes, incomplete transurethral resection of bladder tumor (TURBT) and incomplete response to radio-chemotherapy. The analyzed follow-up guidelines varied slightly in terms of the number, timing, and types of investigations, but overall, the recommendations were similar. CONCLUSION: Randomized prospective studies should focus on evaluating the impact of specific follow-up protocols on oncological and functional outcomes following trimodal treatment for muscle-invasive bladder cancer. It is crucial to evaluate personalized adaption of follow-up protocols based on established risk factors, as there is potential for improved patient outcomes and resource allocation.	bladder
Inhibition of JNK Signaling Overcomes Cancer-Associated Fibroblast-Mediated Immunosuppression and Enhances the Efficacy of Immunotherapy in Bladder Cancer.	Currently, only 20% to 40% of patients with cancer benefit from immune checkpoint inhibitors. Understanding the mechanisms underlying the immunosuppressive tumor microenvironment (TME) and characterizing dynamic changes in the immunologic landscape during treatment are critical for improving responsiveness to immunotherapy. In this study, we identified JNK signaling in cancer-associated fibroblasts (CAF) as a regulator of the immunosuppressive TME. Single-cell RNA sequencing of bladder cancer samples treated with a JNK inhibitor revealed enhanced cytotoxicity and effector functions of CD8+ T cells. In untreated tumors, CAFs interacted frequently with CD8+ T cells and mediated their exhaustion. JNK inhibition abrogated the immunosuppression function of CAFs by downregulating the expression of thymic stromal lymphopoietin (TSLP), thereby restoring CD8+ T-cell cytotoxicity. In addition, blockade of CAF-derived TSLP in combination with anti-PD-1 treatment promoted tumor elimination by CD8+ T cells in vivo. Collectively, these results indicate that JNK signaling plays an important immunosuppressive role in the TME by promoting expression of TSLP in CAFs and suggest that inhibiting JNK signaling could be a promising immunotherapeutic strategy for cancer treatment. Significance: JNK signaling promotes the secretion of TSLP by bladder cancer-associated fibroblasts to impede CD8+ T-cell activity, which can be circumvented by combination treatment targeting JNK signaling and PD-1.	bladder
Development and validation of a model to predict the outcomes of radical cystectomy in patients with bladder cancer.	OBJECTIVES: This study aims to develop a prognostic model that estimates the post-operative risk of cancer-specific mortality in patients with bladder cancer who underwent radical cystectomy (RC). METHODS: We analyzed the data from patients with bladder cancer who had undergone radical cystectomy without receiving adjuvant chemotherapy across 36 institutions in the Japan Urological Oncology Group. The data were randomly split into training (N = 1348) and validation sets (N = 674) in a 2:1 ratio. Twenty-five variables were analyzed, and a multivariable Cox regression model predicting cancer-specific mortality was developed and validated. Prognostic scores were categorized into good and poor prognostic groups based on the upper tertile. The performance of the model was compared against the CheckMate 274 risk classification as a reference, which is used for determining the indication of adjuvant nivolumab therapy. RESULTS: The final model incorporated eight variables. In the validation set, it outperformed the CheckMate 274 risk classification with superior time-dependent area under the curves (5-year: 0.81 vs. 0.67) and was well-calibrated. Furthermore, our model reclassified 27.8% of patients categorized as high-risk by the CheckMate 274 risk classification into the good prognosis group. CONCLUSIONS: We developed and validated a prognostic model for patients with bladder cancer who underwent RC. This model will be beneficial in identifying patients with poor prognosis and those who are potential candidates for clinical trials of adjuvant therapy.	bladder
An evaluation of durvalumab across the spectrum of urothelial carcinoma.	INTRODUCTION: Urothelial carcinoma is a common malignancy affecting the urinary system, with the spectrum of disease encompassing non-muscle invasive, muscle-invasive and metastatic disease. On a background of almost half a century of immunogenic management with BCG, various immune checkpoint inhibitors, including durvalumab, have now demonstrated clinical efficacy in the treatment of urothelial carcinoma. AREAS COVERED: This article reviews the available literature on durvalumab in the treatment of urothelial carcinoma for all stages of the disease including mechanisms of action, pharmacokinetics, efficacy and safety and covers a broad portfolio of reported and ongoing trials. EXPERT OPINION: The management of UC is rapidly evolving, which is reflected in the diverse range of upcoming pivotal trials incorporating durvalumab with additional immunomodulatory agents and therapeutics targeting key oncogenic pathways, each with the potential to change the standard of care. As the complexity of UC management increases, future efforts should be directed at identifying better predictive biomarkers and selecting rational synergistic combinations from the novel treatments available. This will allow the addressing of existing gaps, facilitate the exploitation of new techniques of treatment delivery and ultimately deliver more personalized and efficacious care to the individual patient.	bladder
Nomograms to Appraise The Risk of Chronic Kidney Disease After Radical Cystectomy: Shifting The Focus to Prevention.	INTRODUCTION: Our objectives were to analyse the incidence of changes in renal function after radical cystectomy (RC) and determine the factors responsible for those changes, as a basis for rethinking strategies to ensure early detection and development of a risk-adapted approach. PATIENTS AND METHODS: A single-centre retrospective study included 316 patients who underwent RC between 2010 and 2019. A competing risk Cox model, whereby death from any cause was treated as a censoring event, was used to establish nomograms to analyze the prognostic factors for CKD at 2 and 5 years. The nomograms were validated based on discrimination using the C-index, calibration plots and analysis of net benefit from decision curves. RESULTS: During a median follow-up of 48.73 months (0.13-156.67), 138 patients (43.7%) developed CKD. The probability of CKD development at 2 and 5 years was 41.3% (95% CI, 35.8-47.2) and 48.5% (95% CI, 42.8-54.6), respectively. Hypertension (HR 1.69, 95% CI, 1.23-2.34), prior hydronephrosis (HR 1.62, 95% CI, 1.17-2.25), acute kidney injury (AKI) during the immediate postoperative period (HR 1.88, 95% CI, 1.35-2.61) and readmission due to urinary tract infection (HR 1.41, 95% CI, 1.01-1.96) were predictors of 2-year CKD. Hydronephrosis at follow-up computed tomography (HR 2.21, 95% CI, 1.60-3.07), prior hydronephrosis (HR 1.54, 95% CI, 1.09-2.15), AKI during the immediate postoperative period (HR 1.77, 95% CI, 1.27-2.46) and hypertension (HR 1.60, 95% CI, 1.16-2.21) were predictors for 5-year CKD. Prior eGFR ≥ 90 mL/min/1.73 m(2) was a protective factor (HR 0.50, 95% CI, 0.32-0.80 and HR 0.48, 95% CI, 0.30-0.78 for 2- and 5-year CKD, respectively). The resulting nomograms were based on these prognostic factors. CONCLUSION: Almost half of the patients had developed CKD at 5 years. Thus, it is crucial to identify patients at risk of developing CKD in order to initiate renal function-sparing measures and tailor follow-up protocols. The proposed nomograms effectively predicted CKD in these patients.	bladder
Liquid-liquid phase separation-related genes associated with prognosis, tumor microenvironment characteristics, and tumor cell features in bladder cancer.	OBJECTIVE: This study aimed to explore the Liquid-liquid phase separation (LLPS)-related genes associated with the prognosis of bladder cancer (BCa) and assess the potential application of LLPS-related prognostic signature for predicting prognosis in BCa patients. METHODS: Clinical information and transcriptome data of BCa patients were extracted from the Cancer Genome Atlas-BLCA (TCGA-BLCA) database and the GSE13507 database. Furthermore, 108 BCa patients who received treatment at our institution were subjected to a retrospective analysis. The least absolute shrinkage and selection operator (LASSO) analysis was performed to develop an LLPS-related prognostic signature for BCa. The CCK8, wound healing and Transwell assays were performed. RESULTS: Based on 62 differentially expressed LLPS-related genes (DELRGs), three DELRGs were screened by LASSO analysis including kallikrein-related peptidase 5 (KLK5), monoacylglycerol O-acyltransferase 2 (MOGAT2) and S100 calcium-binding protein A7 (S100A7). Based on three DELRGs, a novel LLPS-related prognostic signature was constructed for individualized prognosis assessment. Kaplan-Meier curve analyses showed that LLPS-related prognostic signature was significantly correlated with overall survival (OS) of BCa. ROC analyses demonstrated the LLPS-related prognostic signature performed well in predicting the prognosis of BCa patients in the training group (the area under the curve (AUC) = 0.733), which was externally verified in the validation cohort 1 (AUC = 0.794) and validation cohort 2 (AUC = 0.766). Further experiments demonstrated that inhibiting KLK5 could affect the proliferation, migration, and invasion of BCa cells. CONCLUSIONS: In this study, a novel LLPS-related prognostic signature was successfully developed and validated, demonstrating strong performance in predicting the prognosis of BCa patients.	bladder